I pretty sure if you use the hotlink protection feature in the Cpanel it will edit your .htaccess file. As a matter of fact, I once lost my .htaccess file by enabling Hotlink protection through the Cpanel because it overwrote the file rather than appended it. Backup before you try. 🙂
Use the cpanel method first. Then you can look into your .htaccess file to see how the format is supposed to be.
A lot of the cpanel methods are editing the .htaccess file. The drawback is they are plain entries. The plus is you can see how Things Are Supposed To Be(tm), and you can customize the file by hand afterwards.